DNA diversification in two Sinorhizobium species

Abstract

The comparative analysis of genomic characteristics and single-nucleotide polymorphism patterns from large fragments borne on different replicons of Sinorhizobium spp. genomes clearly demonstrate that DNA recombination among closely related bacteria is a major event in the diversification of this genome, especially in pSymA, resulting in mosaic structure.

FIG. 1.

Genome-wide PCR analysis in two genomes. Three replicons are shown according to their sizes in strain S. meliloti 1021. The inner circle in each replicon corresponds to S. meliloti 41, and the outer circle corresponds to S. medicae M3. Blue segments represent PCR products with the expected size of 5 kb. Red segments represent products with sizes differing from those of S. meliloti 1021; in these cases the length of each product is proportional to the height of the segment. Regions without colored segments indicate that PCR products were not obtained. Black arrowheads point out regions selected for sequencing and SNP analysis.

FIG. 2.

Distribution of SNPs of 10 fragments from 10 strains. Strains are reported in Table 1. Species abbreviations: Smel, S. meliloti; Smed, S. medicae. Regions a1, a2, and b1, etc., are the sequenced PCR products. The letters a, b, and c stand for pSymA, pSymB, and the chromosome, respectively. Sequence alignments of each region were performed using Clustal X, and a consensus sequence was obtained for each nucleotide position. The SNPs in the same position were decided by the divergence from consensus. The results of the distribution of SNPs for each fragment are plotted as bars to show the number of nucleotides differing from the consensus in consecutive windows of 300 nucleotides for each region. The rules for the color code for each region are as follows: red, blue, dark green, orange, and yellow represent identical nucleotide variations from the consensus in different strains (with five or more differences); in addition, the divergences shared only by S. medicae strains but different from the consensus are shown in light green; black represents nucleotides differing from the consensus shared by at least two strains in cases where any two strains do not share more than 5 nucleotides differing from the consensus in the whole 5-kb region; gray represents nucleotides differing from the consensus present in only one of the strains. Although the rules of the color code are the same for the different regions, the colors are valid only for each specific DNA region.